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Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation.

Simon Penel1, Hugo Menet1, Théo Tricou1

  • 1Laboratoire de Biométrie et Biologie Evolutive/UMR5558, CNRS/UCBL, Villeurbanne 69622, France.

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Summary

Thirdkind is a new command-line tool that visualizes evolutionary reconciliations, including complex 3-level host-symbiont-gene relationships. This software generates SVG files from standard recPhyloXML input, offering a versatile solution for evolutionary biologists.

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Computational biology

Background:

  • Phylogenetic reconciliation is crucial for understanding host-symbiont and species-gene evolutionary relationships.
  • Existing tools lack a generic interface for visualizing reconciliation results across diverse biological comparisons.
  • There is a specific need for tools capable of visualizing complex, multi-level nested reconciliations (e.g., host/symbiont/gene).

Purpose of the Study:

  • To develop a novel, user-friendly software tool for visualizing phylogenetic reconciliations.
  • To address the limitations of current tools by providing a generic and versatile visualization solution.
  • To enable the visualization of complex, three-level nested reconciliations.

Main Methods:

  • Developed Thirdkind, a command-line software.
  • Implemented input compatibility with the standard recPhyloXML format.
  • Designed the software to generate Scalable Vector Graphics (SVG) output files.

Main Results:

  • Thirdkind provides a light and easy-to-install solution for visualizing evolutionary reconciliations.
  • The software successfully generates SVG visualizations, supporting both simple and complex 3-level reconciliations.
  • It is compatible with most reconciliation software due to its use of the recPhyloXML standard.

Conclusions:

  • Thirdkind offers a significant advancement in visualizing complex evolutionary relationships.
  • Its generic nature and ease of use make it broadly applicable in evolutionary studies.
  • The tool facilitates a deeper understanding of co-evolutionary processes across multiple biological levels.